Per chromosome imputation report for cohort Group2.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 31.5.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 12653691 | 73.298 |
| 0.1 | 1220307 | 7.069 |
| 0.2 | 812775 | 4.708 |
| 0.3 | 618217 | 3.581 |
| 0.4 | 497794 | 2.884 |
| 0.5 | 407021 | 2.358 |
| 0.6 | 350248 | 2.029 |
| 0.7 | 291848 | 1.691 |
| 0.8 | 244465 | 1.416 |
| 0.9 | 166909 | 0.967 |
| Total | 17263275 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 751881 | 4.355 |
| 0.4 | 832242 | 4.821 |
| 0.5 | 1067249 | 6.182 |
| 0.6 | 1526125 | 8.840 |
| 0.7 | 2109598 | 12.220 |
| 0.8 | 2792620 | 16.177 |
| 0.9 | 8155765 | 47.243 |
| 1.0 | 27795 | 0.161 |
| Total | 17263275 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 966464 | 73.7469 |
| 0.1 | 90432 | 6.9005 |
| 0.2 | 58264 | 4.4459 |
| 0.3 | 45461 | 3.4689 |
| 0.4 | 37557 | 2.8658 |
| 0.5 | 30976 | 2.3637 |
| 0.6 | 26908 | 2.0532 |
| 0.7 | 21701 | 1.6559 |
| 0.8 | 18812 | 1.4355 |
| 0.9 | 13940 | 1.0637 |
| Total | 1310515 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 59333 | 4.5275 |
| 0.4 | 64640 | 4.9324 |
| 0.5 | 82302 | 6.2801 |
| 0.6 | 118549 | 9.0460 |
| 0.7 | 164725 | 12.5695 |
| 0.8 | 211431 | 16.1334 |
| 0.9 | 607588 | 46.3625 |
| 1.0 | 1947 | 0.1486 |
| Total | 1310515 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1062986 | 73.9518 |
| 0.1 | 100913 | 7.0205 |
| 0.2 | 65457 | 4.5538 |
| 0.3 | 49636 | 3.4532 |
| 0.4 | 38709 | 2.6930 |
| 0.5 | 33285 | 2.3156 |
| 0.6 | 28755 | 2.0005 |
| 0.7 | 23487 | 1.6340 |
| 0.8 | 20060 | 1.3956 |
| 0.9 | 14116 | 0.9820 |
| Total | 1437404 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 61372 | 4.2696 |
| 0.4 | 67097 | 4.6679 |
| 0.5 | 86624 | 6.0264 |
| 0.6 | 124240 | 8.6434 |
| 0.7 | 174464 | 12.1374 |
| 0.8 | 234141 | 16.2892 |
| 0.9 | 687501 | 47.8294 |
| 1.0 | 1965 | 0.1367 |
| Total | 1437404 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 891164 | 73.3694 |
| 0.1 | 87679 | 7.2186 |
| 0.2 | 55340 | 4.5561 |
| 0.3 | 42641 | 3.5106 |
| 0.4 | 35909 | 2.9564 |
| 0.5 | 29176 | 2.4021 |
| 0.6 | 24085 | 1.9829 |
| 0.7 | 20729 | 1.7066 |
| 0.8 | 16614 | 1.3678 |
| 0.9 | 11289 | 0.9294 |
| Total | 1214626 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49910 | 4.1091 |
| 0.4 | 55343 | 4.5564 |
| 0.5 | 70639 | 5.8157 |
| 0.6 | 103786 | 8.5447 |
| 0.7 | 147367 | 12.1327 |
| 0.8 | 193245 | 15.9098 |
| 0.9 | 591561 | 48.7031 |
| 1.0 | 2775 | 0.2285 |
| Total | 1214626 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 880054 | 72.6623 |
| 0.1 | 82339 | 6.7984 |
| 0.2 | 61750 | 5.0984 |
| 0.3 | 44561 | 3.6792 |
| 0.4 | 34022 | 2.8091 |
| 0.5 | 27985 | 2.3106 |
| 0.6 | 24660 | 2.0361 |
| 0.7 | 21829 | 1.8023 |
| 0.8 | 20015 | 1.6526 |
| 0.9 | 13941 | 1.1510 |
| Total | 1211156 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49978 | 4.1265 |
| 0.4 | 54419 | 4.4931 |
| 0.5 | 70545 | 5.8246 |
| 0.6 | 100315 | 8.2826 |
| 0.7 | 143599 | 11.8564 |
| 0.8 | 193523 | 15.9784 |
| 0.9 | 596963 | 49.2887 |
| 1.0 | 1814 | 0.1498 |
| Total | 1211156 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 809036 | 73.4824 |
| 0.1 | 76612 | 6.9584 |
| 0.2 | 52758 | 4.7919 |
| 0.3 | 40736 | 3.6999 |
| 0.4 | 31655 | 2.8751 |
| 0.5 | 24052 | 2.1846 |
| 0.6 | 22904 | 2.0803 |
| 0.7 | 18065 | 1.6408 |
| 0.8 | 15241 | 1.3843 |
| 0.9 | 9934 | 0.9023 |
| Total | 1100993 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 45207 | 4.1060 |
| 0.4 | 49071 | 4.4570 |
| 0.5 | 62687 | 5.6937 |
| 0.6 | 92436 | 8.3957 |
| 0.7 | 132589 | 12.0427 |
| 0.8 | 178904 | 16.2493 |
| 0.9 | 538659 | 48.9248 |
| 1.0 | 1440 | 0.1308 |
| Total | 1100993 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 789120 | 72.6253 |
| 0.1 | 80089 | 7.3709 |
| 0.2 | 52697 | 4.8499 |
| 0.3 | 40869 | 3.7613 |
| 0.4 | 32865 | 3.0247 |
| 0.5 | 26260 | 2.4168 |
| 0.6 | 22717 | 2.0907 |
| 0.7 | 16931 | 1.5582 |
| 0.8 | 15154 | 1.3947 |
| 0.9 | 9861 | 0.9075 |
| Total | 1086563 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 41965 | 3.8622 |
| 0.4 | 45623 | 4.1988 |
| 0.5 | 58133 | 5.3502 |
| 0.6 | 84977 | 7.8207 |
| 0.7 | 120028 | 11.0466 |
| 0.8 | 164236 | 15.1152 |
| 0.9 | 568000 | 52.2749 |
| 1.0 | 3601 | 0.3314 |
| Total | 1086563 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 709376 | 72.9805 |
| 0.1 | 69807 | 7.1817 |
| 0.2 | 47705 | 4.9079 |
| 0.3 | 35463 | 3.6484 |
| 0.4 | 28956 | 2.9790 |
| 0.5 | 23917 | 2.4606 |
| 0.6 | 18839 | 1.9382 |
| 0.7 | 16487 | 1.6962 |
| 0.8 | 12453 | 1.2812 |
| 0.9 | 9005 | 0.9264 |
| Total | 972008 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40973 | 4.2153 |
| 0.4 | 45175 | 4.6476 |
| 0.5 | 58321 | 6.0001 |
| 0.6 | 84152 | 8.6575 |
| 0.7 | 118484 | 12.1896 |
| 0.8 | 158916 | 16.3492 |
| 0.9 | 464928 | 47.8317 |
| 1.0 | 1059 | 0.1089 |
| Total | 972008 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 700672 | 73.8915 |
| 0.1 | 64523 | 6.8045 |
| 0.2 | 44129 | 4.6538 |
| 0.3 | 32400 | 3.4168 |
| 0.4 | 27786 | 2.9303 |
| 0.5 | 21621 | 2.2801 |
| 0.6 | 19308 | 2.0362 |
| 0.7 | 15456 | 1.6300 |
| 0.8 | 13495 | 1.4232 |
| 0.9 | 8855 | 0.9338 |
| Total | 948245 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 39605 | 4.1767 |
| 0.4 | 43964 | 4.6364 |
| 0.5 | 55421 | 5.8446 |
| 0.6 | 79920 | 8.4282 |
| 0.7 | 111709 | 11.7806 |
| 0.8 | 151465 | 15.9732 |
| 0.9 | 464501 | 48.9853 |
| 1.0 | 1660 | 0.1751 |
| Total | 948245 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 530159 | 73.3257 |
| 0.1 | 53789 | 7.4395 |
| 0.2 | 34106 | 4.7172 |
| 0.3 | 24676 | 3.4129 |
| 0.4 | 21012 | 2.9061 |
| 0.5 | 15505 | 2.1445 |
| 0.6 | 14616 | 2.0215 |
| 0.7 | 12049 | 1.6665 |
| 0.8 | 9961 | 1.3777 |
| 0.9 | 7146 | 0.9884 |
| Total | 723019 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 29863 | 4.1303 |
| 0.4 | 33248 | 4.5985 |
| 0.5 | 43454 | 6.0101 |
| 0.6 | 62832 | 8.6902 |
| 0.7 | 89399 | 12.3647 |
| 0.8 | 120564 | 16.6751 |
| 0.9 | 342617 | 47.3870 |
| 1.0 | 1042 | 0.1441 |
| Total | 723019 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 611961 | 72.9377 |
| 0.1 | 60678 | 7.2320 |
| 0.2 | 39897 | 4.7552 |
| 0.3 | 28872 | 3.4412 |
| 0.4 | 24831 | 2.9595 |
| 0.5 | 20732 | 2.4710 |
| 0.6 | 16761 | 1.9977 |
| 0.7 | 14540 | 1.7330 |
| 0.8 | 12649 | 1.5076 |
| 0.9 | 8098 | 0.9652 |
| Total | 839019 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 34278 | 4.0855 |
| 0.4 | 38206 | 4.5537 |
| 0.5 | 48704 | 5.8049 |
| 0.6 | 69793 | 8.3184 |
| 0.7 | 98635 | 11.7560 |
| 0.8 | 135049 | 16.0961 |
| 0.9 | 413190 | 49.2468 |
| 1.0 | 1164 | 0.1387 |
| Total | 839019 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 613010 | 73.1766 |
| 0.1 | 58073 | 6.9323 |
| 0.2 | 36816 | 4.3948 |
| 0.3 | 31124 | 3.7154 |
| 0.4 | 23517 | 2.8073 |
| 0.5 | 20687 | 2.4695 |
| 0.6 | 18655 | 2.2269 |
| 0.7 | 14203 | 1.6954 |
| 0.8 | 12440 | 1.4850 |
| 0.9 | 9188 | 1.0968 |
| Total | 837713 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33533 | 4.0029 |
| 0.4 | 36465 | 4.3529 |
| 0.5 | 46964 | 5.6062 |
| 0.6 | 70529 | 8.4192 |
| 0.7 | 101522 | 12.1189 |
| 0.8 | 135461 | 16.1703 |
| 0.9 | 410981 | 49.0599 |
| 1.0 | 2258 | 0.2695 |
| Total | 837713 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 584696 | 73.1809 |
| 0.1 | 56462 | 7.0668 |
| 0.2 | 36010 | 4.5070 |
| 0.3 | 30382 | 3.8026 |
| 0.4 | 23211 | 2.9051 |
| 0.5 | 18891 | 2.3644 |
| 0.6 | 15973 | 1.9992 |
| 0.7 | 12707 | 1.5904 |
| 0.8 | 12535 | 1.5689 |
| 0.9 | 8106 | 1.0146 |
| Total | 798973 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33727 | 4.2213 |
| 0.4 | 37131 | 4.6473 |
| 0.5 | 47546 | 5.9509 |
| 0.6 | 68881 | 8.6212 |
| 0.7 | 96225 | 12.0436 |
| 0.8 | 129524 | 16.2113 |
| 0.9 | 384677 | 48.1464 |
| 1.0 | 1262 | 0.1580 |
| Total | 798973 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 437413 | 72.1833 |
| 0.1 | 43125 | 7.1166 |
| 0.2 | 27956 | 4.6134 |
| 0.3 | 22486 | 3.7107 |
| 0.4 | 17349 | 2.8630 |
| 0.5 | 15918 | 2.6268 |
| 0.6 | 12669 | 2.0907 |
| 0.7 | 11188 | 1.8463 |
| 0.8 | 9877 | 1.6299 |
| 0.9 | 7994 | 1.3192 |
| Total | 605975 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 24437 | 4.0327 |
| 0.4 | 26700 | 4.4061 |
| 0.5 | 34626 | 5.7141 |
| 0.6 | 51751 | 8.5401 |
| 0.7 | 74083 | 12.2254 |
| 0.8 | 97733 | 16.1282 |
| 0.9 | 295812 | 48.8159 |
| 1.0 | 833 | 0.1375 |
| Total | 605975 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 398820 | 73.5714 |
| 0.1 | 38978 | 7.1904 |
| 0.2 | 26023 | 4.8005 |
| 0.3 | 18191 | 3.3557 |
| 0.4 | 15216 | 2.8069 |
| 0.5 | 11911 | 2.1973 |
| 0.6 | 10162 | 1.8746 |
| 0.7 | 9000 | 1.6603 |
| 0.8 | 8153 | 1.5040 |
| 0.9 | 5632 | 1.0389 |
| Total | 542086 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 22570 | 4.1635 |
| 0.4 | 25119 | 4.6338 |
| 0.5 | 32858 | 6.0614 |
| 0.6 | 48048 | 8.8635 |
| 0.7 | 65796 | 12.1376 |
| 0.8 | 87450 | 16.1321 |
| 0.9 | 259793 | 47.9247 |
| 1.0 | 452 | 0.0834 |
| Total | 542086 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 346716 | 73.1708 |
| 0.1 | 33034 | 6.9715 |
| 0.2 | 22327 | 4.7119 |
| 0.3 | 16930 | 3.5729 |
| 0.4 | 14674 | 3.0968 |
| 0.5 | 11408 | 2.4075 |
| 0.6 | 9079 | 1.9160 |
| 0.7 | 7903 | 1.6678 |
| 0.8 | 6452 | 1.3616 |
| 0.9 | 5322 | 1.1232 |
| Total | 473845 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 22696 | 4.7898 |
| 0.4 | 26129 | 5.5143 |
| 0.5 | 32770 | 6.9158 |
| 0.6 | 44965 | 9.4894 |
| 0.7 | 59486 | 12.5539 |
| 0.8 | 78168 | 16.4965 |
| 0.9 | 209187 | 44.1467 |
| 1.0 | 444 | 0.0937 |
| Total | 473845 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 391283 | 74.0225 |
| 0.1 | 37987 | 7.1863 |
| 0.2 | 23001 | 4.3513 |
| 0.3 | 18675 | 3.5329 |
| 0.4 | 14487 | 2.7406 |
| 0.5 | 12304 | 2.3277 |
| 0.6 | 10736 | 2.0310 |
| 0.7 | 9282 | 1.7560 |
| 0.8 | 6817 | 1.2896 |
| 0.9 | 4028 | 0.7620 |
| Total | 528600 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 25521 | 4.8280 |
| 0.4 | 28407 | 5.3740 |
| 0.5 | 36272 | 6.8619 |
| 0.6 | 52212 | 9.8774 |
| 0.7 | 70134 | 13.2679 |
| 0.8 | 91440 | 17.2985 |
| 0.9 | 224220 | 42.4177 |
| 1.0 | 394 | 0.0745 |
| Total | 528600 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 331403 | 73.4966 |
| 0.1 | 30521 | 6.7688 |
| 0.2 | 23106 | 5.1243 |
| 0.3 | 15649 | 3.4705 |
| 0.4 | 13171 | 2.9210 |
| 0.5 | 11149 | 2.4726 |
| 0.6 | 8848 | 1.9623 |
| 0.7 | 8260 | 1.8319 |
| 0.8 | 5626 | 1.2477 |
| 0.9 | 3176 | 0.7044 |
| Total | 450909 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 23201 | 5.1454 |
| 0.4 | 26227 | 5.8165 |
| 0.5 | 35253 | 7.8182 |
| 0.6 | 47371 | 10.5057 |
| 0.7 | 60008 | 13.3082 |
| 0.8 | 75188 | 16.6748 |
| 0.9 | 183247 | 40.6395 |
| 1.0 | 414 | 0.0918 |
| Total | 450909 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 349861 | 72.9762 |
| 0.1 | 34521 | 7.2006 |
| 0.2 | 23289 | 4.8578 |
| 0.3 | 17632 | 3.6778 |
| 0.4 | 14135 | 2.9484 |
| 0.5 | 10703 | 2.2325 |
| 0.6 | 9769 | 2.0377 |
| 0.7 | 8042 | 1.6775 |
| 0.8 | 6556 | 1.3675 |
| 0.9 | 4910 | 1.0242 |
| Total | 479418 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 21172 | 4.4162 |
| 0.4 | 23905 | 4.9863 |
| 0.5 | 32032 | 6.6814 |
| 0.6 | 45169 | 9.4216 |
| 0.7 | 61073 | 12.7390 |
| 0.8 | 80345 | 16.7589 |
| 0.9 | 215252 | 44.8986 |
| 1.0 | 470 | 0.0980 |
| Total | 479418 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 268898 | 72.8186 |
| 0.1 | 29278 | 7.9286 |
| 0.2 | 18716 | 5.0684 |
| 0.3 | 13440 | 3.6396 |
| 0.4 | 9671 | 2.6189 |
| 0.5 | 8854 | 2.3977 |
| 0.6 | 6921 | 1.8742 |
| 0.7 | 6206 | 1.6806 |
| 0.8 | 4606 | 1.2473 |
| 0.9 | 2681 | 0.7260 |
| Total | 369271 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 19536 | 5.2904 |
| 0.4 | 23143 | 6.2672 |
| 0.5 | 28491 | 7.7155 |
| 0.6 | 38985 | 10.5573 |
| 0.7 | 48765 | 13.2057 |
| 0.8 | 61371 | 16.6195 |
| 0.9 | 148516 | 40.2187 |
| 1.0 | 464 | 0.1257 |
| Total | 369271 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 275060 | 73.3620 |
| 0.1 | 26908 | 7.1767 |
| 0.2 | 18260 | 4.8702 |
| 0.3 | 13519 | 3.6057 |
| 0.4 | 11255 | 3.0019 |
| 0.5 | 8611 | 2.2967 |
| 0.6 | 7984 | 2.1294 |
| 0.7 | 5788 | 1.5437 |
| 0.8 | 4644 | 1.2386 |
| 0.9 | 2906 | 0.7751 |
| Total | 374935 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17135 | 4.5701 |
| 0.4 | 19546 | 5.2132 |
| 0.5 | 25660 | 6.8439 |
| 0.6 | 36368 | 9.6998 |
| 0.7 | 47911 | 12.7785 |
| 0.8 | 62561 | 16.6858 |
| 0.9 | 165468 | 44.1324 |
| 1.0 | 286 | 0.0763 |
| Total | 374935 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 164578 | 72.1431 |
| 0.1 | 15793 | 6.9229 |
| 0.2 | 10467 | 4.5882 |
| 0.3 | 9211 | 4.0377 |
| 0.4 | 7017 | 3.0759 |
| 0.5 | 6138 | 2.6906 |
| 0.6 | 4857 | 2.1291 |
| 0.7 | 4436 | 1.9445 |
| 0.8 | 3999 | 1.7530 |
| 0.9 | 1631 | 0.7150 |
| Total | 228127 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 11221 | 4.9188 |
| 0.4 | 12180 | 5.3391 |
| 0.5 | 15789 | 6.9211 |
| 0.6 | 22363 | 9.8029 |
| 0.7 | 28610 | 12.5413 |
| 0.8 | 37684 | 16.5189 |
| 0.9 | 100073 | 43.8672 |
| 1.0 | 207 | 0.0907 |
| Total | 228127 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 159778 | 73.1075 |
| 0.1 | 15525 | 7.1036 |
| 0.2 | 10987 | 5.0272 |
| 0.3 | 7860 | 3.5964 |
| 0.4 | 6734 | 3.0812 |
| 0.5 | 5084 | 2.3262 |
| 0.6 | 4487 | 2.0531 |
| 0.7 | 4002 | 1.8311 |
| 0.8 | 2644 | 1.2098 |
| 0.9 | 1451 | 0.6639 |
| Total | 218552 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 11667 | 5.3383 |
| 0.4 | 13063 | 5.9771 |
| 0.5 | 16312 | 7.4637 |
| 0.6 | 21997 | 10.0649 |
| 0.7 | 28112 | 12.8628 |
| 0.8 | 35015 | 16.0214 |
| 0.9 | 92221 | 42.1964 |
| 1.0 | 165 | 0.0755 |
| Total | 218552 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 381183 | 74.5484 |
| 0.1 | 33241 | 6.5010 |
| 0.2 | 23714 | 4.6378 |
| 0.3 | 17803 | 3.4818 |
| 0.4 | 14055 | 2.7488 |
| 0.5 | 11854 | 2.3183 |
| 0.6 | 10555 | 2.0643 |
| 0.7 | 9557 | 1.8691 |
| 0.8 | 5662 | 1.1073 |
| 0.9 | 3699 | 0.7234 |
| Total | 511323 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 32981 | 6.4501 |
| 0.4 | 37441 | 7.3224 |
| 0.5 | 45846 | 8.9662 |
| 0.6 | 56486 | 11.0470 |
| 0.7 | 66874 | 13.0786 |
| 0.8 | 79206 | 15.4904 |
| 0.9 | 190810 | 37.3169 |
| 1.0 | 1679 | 0.3284 |
| Total | 511323 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering